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Magnesium in PDB 3iki: 5-Sme-Du Containing Dna Octamer

Protein crystallography data

The structure of 5-Sme-Du Containing Dna Octamer, PDB code: 3iki was solved by J.Sheng, A.E.A.Hassan, W.Zhang, J.Gan, Z.Huang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.32 / 1.38
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 42.882, 42.882, 23.687, 90.00, 90.00, 90.00
R / Rfree (%) 17.8 / 19.4

Magnesium Binding Sites:

The binding sites of Magnesium atom in the 5-Sme-Du Containing Dna Octamer (pdb code 3iki). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the 5-Sme-Du Containing Dna Octamer, PDB code: 3iki:

Magnesium binding site 1 out of 1 in 3iki

Go back to Magnesium Binding Sites List in 3iki
Magnesium binding site 1 out of 1 in the 5-Sme-Du Containing Dna Octamer


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of 5-Sme-Du Containing Dna Octamer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg11

b:31.3
occ:1.00
OP2 A:DG3 2.1 16.5 1.0
O A:HOH36 2.6 22.0 1.0
O A:HOH45 2.7 23.7 1.0
P A:DG3 3.4 15.7 1.0
C8 A:DG3 3.4 10.0 1.0
C3' A:UMS2 3.5 10.5 1.0
C5' A:DG3 3.5 13.7 1.0
O A:HOH32 3.7 20.0 1.0
N7 A:DG3 3.9 9.9 1.0
O3' A:UMS2 3.9 12.8 1.0
O5' A:DG3 3.9 15.2 1.0
O5' A:UMS2 4.1 8.9 1.0
C6 A:UMS2 4.1 9.1 1.0
C2' A:UMS2 4.2 10.0 1.0
O4' A:DG3 4.4 12.4 1.0
C5 A:UMS2 4.5 9.6 1.0
N1 A:UMS2 4.6 9.2 1.0
C4' A:DG3 4.6 13.2 1.0
O A:HOH26 4.6 21.2 1.0
OP2 A:UMS2 4.6 10.5 1.0
N9 A:DG3 4.6 10.2 1.0
C4' A:UMS2 4.6 9.1 1.0
OP1 A:DG3 4.7 17.1 1.0
C5' A:UMS2 4.8 8.8 1.0
C1' A:UMS2 4.9 8.9 1.0
P A:UMS2 4.9 9.1 1.0

Reference:

J.Sheng, W.Zhang, A.E.Hassan, J.Gan, A.S.Soares, S.Geng, Y.Ren, Z.Huang. Hydrogen Bond Formation Between the Naturally Modified Nucleobase and Phosphate Backbone. Nucleic Acids Res. V. 40 8111 2012.
ISSN: ISSN 0305-1048
PubMed: 22641848
DOI: 10.1093/NAR/GKS426
Page generated: Mon Dec 14 08:17:13 2020

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